Protein Synthesis

A gene is a stretch of DNA whose base sequence codes for the amino acid sequence of a polypeptide. Turning that code into a protein takes two stages: transcription, in which the base sequence of the gene is copied into messenger RNA in the nucleus, and translation, in which ribosomes in the cytoplasm read the mRNA and join amino acids in the right order, brought by transfer RNA. This note covers the genetic code, both stages step by step, and the splicing of introns out of eukaryotic RNA. It is one of the most heavily examined topics in AS Biology: expect long "describe" questions, and short questions that ask you to convert between DNA, mRNA, anticodons and amino acids using a codon table.

Genes and the genetic code

There are 20 amino acids but only 4 bases. One base per amino acid would give only 4 combinations, two bases only $4^2 = 16$. Three bases give $4^3 = 64$ combinations, enough for all 20 amino acids. So the code is a triplet code.

The mRNA codon table (first base on the left, second base across the top, third base within each cell):

First base	U	C	A	G
U	UUU Phe UUC Phe UUA Leu UUG Leu	UCU Ser UCC Ser UCA Ser UCG Ser	UAU Tyr UAC Tyr UAA stop UAG stop	UGU Cys UGC Cys UGA stop UGG Trp
C	CUU Leu CUC Leu CUA Leu CUG Leu	CCU Pro CCC Pro CCA Pro CCG Pro	CAU His CAC His CAA Gln CAG Gln	CGU Arg CGC Arg CGA Arg CGG Arg
A	AUU Ile AUC Ile AUA Ile AUG Met (start)	ACU Thr ACC Thr ACA Thr ACG Thr	AAU Asn AAC Asn AAA Lys AAG Lys	AGU Ser AGC Ser AGA Arg AGG Arg
G	GUU Val GUC Val GUA Val GUG Val	GCU Ala GCC Ala GCA Ala GCG Ala	GAU Asp GAC Asp GAA Glu GAG Glu	GGU Gly GGC Gly GGA Gly GGG Gly

You do not need to learn the table; the exam provides whatever part is needed. You must know AUG (start) and that there are three stop codons.

The template and non-transcribed strands

Only one of the two DNA strands of a gene is used to make mRNA.

Because mRNA is complementary to the template strand, it has the same base sequence as the non-transcribed strand, except that it contains U where the DNA has T. (The non-transcribed strand is sometimes called the coding strand for this reason.)

	Example sequence
Non-transcribed strand (DNA)	5′ ATG GCT TTC CAA TGA 3′
Template strand (DNA)	3′ TAC CGA AAG GTT ACT 5′
mRNA (complementary to template)	5′ AUG GCU UUC CAA UGA 3′
Amino acids	Met – Ala – Phe – Gln – stop

Transcription

Transcription takes place in the nucleus. DNA is too large to leave the nucleus and must be protected, so a mobile copy of the gene, mRNA, is made instead.

In eukaryotes, the RNA produced directly by transcription is called the primary transcript (or pre-mRNA). It is modified before it leaves the nucleus.

Splicing: removing introns

Eukaryotic genes contain sections that do not code for amino acids.

Both introns and exons are transcribed, so the primary transcript contains both. Splicing (carried out by complexes of protein and RNA) cuts out the introns and joins the exons end to end. The finished mRNA is shorter and contains only the coding sequence, which can be translated continuously. It then leaves the nucleus through a nuclear pore and travels to a ribosome in the cytoplasm or on the rough endoplasmic reticulum.

Prokaryotic genes do not have introns, so prokaryotes do not splice their RNA; and because they have no nucleus, translation can begin while transcription is still going on.

Translation

Translation takes place at ribosomes in the cytoplasm (free or on the rough ER). The ribosome reads the mRNA codon by codon, and tRNA molecules bring the matching amino acids.

Transfer RNA

Each tRNA molecule is a single strand of RNA, about 80 nucleotides long, folded into a clover-leaf shape held by hydrogen bonds between complementary bases within the strand. It has:

• an anticodon: a sequence of three bases at one end (in a loop) that is complementary to a particular mRNA codon;
• an amino acid binding site at the other end (the 3′ end), where the specific amino acid that corresponds to the anticodon is attached.

Each amino acid is attached to its own tRNA by a specific enzyme, using energy from ATP. This "activates" the amino acid ready for peptide bond formation.

Ribosomes

A ribosome has a small subunit and a large subunit, made of rRNA and protein. It has a groove for the mRNA and room for two tRNA molecules at a time, so it holds two codons (six bases) of the mRNA in place while the amino acids on the two tRNAs are joined.

Several ribosomes can translate the same mRNA molecule at once, one behind the other, forming a polysome, so many copies of the polypeptide are made quickly. After translation, polypeptides made on the rough ER are folded and modified (for example, by adding carbohydrate in the Golgi body) to form functional proteins.

Practice questions

Answers

1. A sequence of nucleotides that forms part of a DNA molecule and codes for a polypeptide.
2. There are 20 amino acids; with 4 bases, a single-base code gives only 4 combinations and a two-base code $4^2 = 16$, too few; a triplet gives $4^3 = 64$, enough to code for all 20.
3. (a) The same codons code for the same amino acids in (almost) all organisms. (b) Most amino acids are coded for by more than one codon/triplet.
4. The template (transcribed) strand is the DNA strand used as the template for transcription; mRNA is complementary to it. The non-transcribed strand is the other strand of the gene; it is not used, and its sequence is the same as the mRNA (with T in place of U).
5. mRNA: 5′ AUG AAA GGC UAA 3′. Polypeptide: Met–Lys–Gly (UAA = stop).
6. Any two: transcription copies only one gene, replication the whole DNA molecule; transcription uses one strand as template, replication both; transcription uses RNA nucleotides (with ribose and uracil), replication DNA nucleotides; transcription uses RNA polymerase, replication DNA polymerase (and helicase, ligase); transcription produces single-stranded RNA, replication two double-stranded DNA molecules; transcription occurs throughout interphase (when the gene is needed), replication only in S phase.
7. A codon is a triplet of bases on mRNA that codes for an amino acid (or start/stop); an anticodon is a triplet of bases on tRNA that is complementary to a codon.
8. Each tRNA carries a specific amino acid (attached at one end, using ATP); its anticodon binds to the complementary codon on the mRNA at the ribosome by complementary base pairing; so the amino acids are brought to the ribosome and placed in the order specified by the sequence of codons; tRNA is released after its amino acid has been joined to the chain, to be reused.
9. $450 \times 3 = 1350$ nucleotides, plus 3 for the stop codon $= 1353$. The gene contains introns (non-coding sequences) between the exons, which are transcribed but removed by splicing; it also has regulatory and non-translated sequences.
10. Any nine: DNA unwinds and hydrogen bonds between bases break (in the region of the gene); one strand is the template strand; free RNA nucleotides pair with complementary bases (A–U, T–A, C–G, G–C); RNA polymerase joins RNA nucleotides with phosphodiester bonds; the primary transcript is spliced: introns removed and exons joined to form mRNA; mRNA leaves the nucleus through a nuclear pore; mRNA attaches to a ribosome (small subunit); translation begins at the start codon AUG; tRNA molecules carry specific amino acids; the anticodon on tRNA pairs with the complementary codon on mRNA; the ribosome holds two tRNAs/two codons; a peptide bond forms between the amino acids (condensation); the ribosome moves along one codon and the first tRNA is released; process repeats until a stop codon is reached and the polypeptide is released; the order of amino acids (primary structure) is determined by the sequence of codons, i.e. by the base sequence of the gene.